HTSMultiQC-cleaning-report

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.24.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        HTSMultiQC-cleaning-report

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-10-23, 11:28 PDT based on data in: /mnt/analysis/cat_users/matt/rnaseq_example/01-HTS_Preproc


        General Statistics

        Showing 0/3 rows and 2/2 columns.
        Sample NameM InputM Output
        NEB_Mixed-10-ng-1_1M_S383
        1.00
        0.41
        NEB_Mixed-10-ng-2_S384
        1.00
        0.41
        NEB_Mixed-10-ng-3_S385
        1.00
        0.41

        HTStream

        HTStream quality control and processing pipeline for High Throughput Sequencing data.URL: https://s4hts.github.io/HTStream

        Processing Overview

        Plots reduction of reads and basepairs across the preprocessing pipeline.

        Created with MultiQC

        hts_Stats_1 Table

        Basic statistics about the reads in a dataset.

        initial stats

        Showing 0/3 rows and 4/4 columns.
        Sample Name% R1 Q30% R2 Q30GC ContentN Content
        NEB_Mixed-10-ng-1_1M_S383
        95.14%
        95.14%
        46.74%
        0.0016%
        NEB_Mixed-10-ng-2_S384
        95.05%
        95.05%
        46.63%
        0.0016%
        NEB_Mixed-10-ng-3_S385
        95.17%
        95.17%
        46.47%
        0.0016%

        hts_Stats_1 PE Read Length

        Distribution of read lengths for each sample.

        Showing 0/3 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        NEB_Mixed-10-ng-1_1M_S383
        151
        151
        NEB_Mixed-10-ng-2_S384
        151
        151
        NEB_Mixed-10-ng-3_S385
        151
        151

        hts_Stats_1 PE Base by Cycle

        Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.

        Created with MultiQC

        hts_Stats_1 PE Quality by Cycle

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        Created with MultiQC

        hts_SeqScreener_1

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        screen phix

        Notice: No sequences were identified in any sample.

        hts_SeqScreener_2

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        count the number of rRNA reads

        Created with MultiQC

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        remove PCR duplicates

        Created with MultiQC

        hts_Overlapper

        Attempts to overlap paired end reads to produce the original fragment, trims adapters, and can correct sequencing errors.

        trim adapters

        Created with MultiQC

        hts_PolyATTrim

        Attempts to trim poly-A and poly-T sequences from the end of reads.

        remove polyAT tails

        Created with MultiQC

        hts_NTrimmer

        Trims reads to the longest subsequence that contains no N's.

        remove any remaining N characters

        Created with MultiQC

        hts_QWindowTrim

        Uses a sliding window approach to remove the low quality ends of reads.

        quality trim the ends of reads

        Created with MultiQC

        hts_LengthFilter

        Discards reads below a minimum length threshold.

        remove reads < 50bp

        Created with MultiQC

        hts_Stats_2 Table

        Basic statistics about the reads in a dataset.

        final stats

        Showing 0/3 rows and 5/5 columns.
        Sample Name% R1 Q30% R2 Q30% SE Q30GC ContentN Content
        NEB_Mixed-10-ng-1_1M_S383
        95.91%
        95.91%
        95.65%
        45.41%
        0.0000%
        NEB_Mixed-10-ng-2_S384
        95.83%
        95.83%
        95.79%
        45.40%
        0.0000%
        NEB_Mixed-10-ng-3_S385
        95.93%
        95.93%
        95.64%
        45.37%
        0.0000%

        hts_Stats_2 PE Read Length

        Distribution of read lengths for each sample.

        Created with MultiQC

        hts_Stats_2 PE Base by Cycle

        Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.

        Created with MultiQC

        hts_Stats_2 PE Quality by Cycle

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        Created with MultiQC

        hts_Stats_2 SE Read Length

        Distribution of read lengths for each sample.

        Created with MultiQC

        hts_Stats_2 SE Base by Cycle

        Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.

        Created with MultiQC

        hts_Stats_2 SE Quality by Cycle

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        Created with MultiQC